The present study investigates the variability of both the delta 13C and the delta 15N stable isotopes in modern and archaeological Ctenomys rodents bone collagen. The purpose of this investigation is to assess the correlation of these isotopes with climate, and thereby reconstruct changes in the Holocene habitat of the Monte Desert. Firstly, the isotopic variability (delta C-1(3) and delta 15N) in contemporary Ctenomys (post-1970 AD) bone collagen is evaluated in relation to climatic variables, with an aim to construct a framework of reference. The strongest correlation was observed between the delta C-1(3) and summer temperatures suggesting that the Ctenomys stable isotopes reliably track warm-season climatic trends. The results obtained are utilized for the purpose of examining the stable isotope ratios (C and N) present within archaeological Ctenomys bone collagen samples (pre 200 years BP) derived from an archaeological site situated within the Monte Desert in Mendoza, Argentina, thereby serving as a case study in the fields of palaeoecology and archaeology. The data demonstrate a trend over the last 5000 years BP, indicating a substantial increase in both delta 13C and delta 15N after 1200 cal years BP. This finding suggests a rise in summer mean temperature. Alternative explanations - such as the ingestion of maize or the impact of human activity - are considered, but the most plausible interpretation appears to be climatic. The aforementioned variations are synchronic with the global climatic trends that are characteristic of the Mediaeval Climatic Anomaly. The utilization of Ctenomys isotopes as a high-resolution palaeoclimatic proxy is hereby proposed, with the potential to disentangle anthropogenic from climatic signals in archaeological contexts. The high temporal resolution of Ctenomys isotopes, enabled by future direct bone dating, enhances their utility. The case study presented herein demonstrates the potential (and limitations) of this approach for the reconstruction of climate and habitat dynamics.